Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014024.1 Corchorus capsularis cultivar CVL-1 contig14045, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 38576
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:10739 original size:25 final size:25

Alignment explanation


    Indices: 10705--10756  Score: 95
    Period size: 25  Copynumber: 2.1  Consensus size: 25

      10695 ACATTTGACT

                                     
      10705 CAAGTGATTAACGTGCAAGCCATAG
          1 CAAGTGATTAACGTGCAAGCCATAG

                      *              
      10730 CAAGTGATTAGCGTGCAAGCCATAG
          1 CAAGTGATTAACGTGCAAGCCATAG

              
      10755 CA
          1 CA

      10757 TGGAAAAACT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19


Consensus pattern (25 bp):   
CAAGTGATTAACGTGCAAGCCATAG

Found at i:31307 original size:6 final size:6

Alignment explanation


    Indices: 31298--31324  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      31288 TTTTATTATT

                                           
      31298 ATTAAA ATTAAA ATTAAA ATTAAA ATT
          1 ATTAAA ATTAAA ATTAAA ATTAAA ATT

      31325 TCTTTTATTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (6 bp):   
ATTAAA

Found at i:31308 original size:33 final size:36

Alignment explanation


    Indices: 31271--31354  Score: 102
    Period size: 33  Copynumber: 2.3  Consensus size: 36

      31261 ATATATTATG

                  *                                
      31271 ATTAAAGTTAAAATTTCTTTTATTATTATTAAAATTAAA
          1 ATTAAAATTAAAATTTC-TTTATTATTATT--AATTAAA

                                                
      31310 ATTAAAATTAAAATTTC-TT-TTATTATT-ATTAAA
          1 ATTAAAATTAAAATTTCTTTATTATTATTAATTAAA

                   *    
      31343 ATTAAAACTAAA
          1 ATTAAAATTAAA

      31355 TCAACATTTG


Statistics
Matches: 43,  Mismatches: 2, Indels: 6
        0.84            0.04        0.12

Matches are distributed among these distances:
  33   17  0.40
  36    8  0.19
  37    2  0.05
  39   16  0.37

ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46


Consensus pattern (36 bp):   
ATTAAAATTAAAATTTCTTTATTATTATTAATTAAA

Found at i:31321 original size:39 final size:39

Alignment explanation


    Indices: 31271--31354  Score: 150
    Period size: 39  Copynumber: 2.2  Consensus size: 39

      31261 ATATATTATG

                  *                                
      31271 ATTAAAGTTAAAATTTCTTTTATTATTATTAAAATTAAA
          1 ATTAAAATTAAAATTTCTTTTATTATTATTAAAATTAAA

                                                   
      31310 ATTAAAATTAAAATTTCTTTTATTATTATTAAAATTAAA
          1 ATTAAAATTAAAATTTCTTTTATTATTATTAAAATTAAA

             *    
      31349 ACTAAA
          1 ATTAAA

      31355 TCAACATTTG


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  39   43  1.00

ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46


Consensus pattern (39 bp):   
ATTAAAATTAAAATTTCTTTTATTATTATTAAAATTAAA

Found at i:37992 original size:2 final size:2

Alignment explanation


    Indices: 37985--38015  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      37975 TATATCCAAC

                                                          
      37985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      38016 TATTTTATAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.